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Identification of Bacterial Communities in Sediments of Poyang Lake, The Kou et al. SpringerPlus (2016) 5:401 DOI 10.1186/s40064-016-2026-7 RESEARCH Open Access Identification of bacterial communities in sediments of Poyang Lake, the largest freshwater lake in China Wenbo Kou1,2, Jie Zhang1, Xinxin Lu3, Yantian Ma1,2, Xiaozhen Mou3* and Lan Wu1,2* Abstract Bacteria play a vital role in various biogeochemical processes in lacustrine sediment ecosystems. This study is among the first to investigate the spatial distribution patterns of bacterial community composition in the sediments of Poy- ang Lake, the largest freshwater lake of China. Sediment samples were collected from the main basins and mouths of major rivers that discharge into the Poyang Lake in May 2011. Quantitative PCR assay and pyrosequencing analysis of 16S rRNA genes showed that the bacteria community abundance and compositions of Poyang Lake sediment varied largely among sampling sites. A total of 25 phyla and 68 bacterial orders were distinguished. Burkholderiales, Gallionel- lales (Beta-proteobacteria), Myxococcales, Desulfuromonadales (Delta-proteobacteria), Sphingobacteriales (Bacteroidetes), Nitrospirales (Nitrospirae), Xanthomonadales (Gamma-proteobacteria) were identified as the major taxa and collectively accounted for over half of annotated sequences. Moreover, correlation analyses suggested that higher loads of total phosphorus and heavy metals (copper, zinc and cadmium) could enhance bacterial abundance in the sediment. Keywords: Bacterial community, Sediment, Poyang Lake, High-throughput sequencing Background Bacterial community composition (BCC) in freshwater Freshwater lakes are one of the most extensively altered lakes has been extensively investigated, partly because its ecosystems on earth due to changes of climate, hydro- potentials in predicting major biogeochemical functions. logic flow and human activities related processes, such as Early studies have shown that lake sediment BCC may be land-use and nutrient inputs (Carpenter et al. 2011). Lake shaped by physicochemical factors, such as temperature, sediments are important grounds for series of biogeo- stream flow (Bernhard et al. 2005), pH (Lindström et al. chemical transformations of essential nutrients (carbon, 2005) and nutrient concentrations (Bai et al. 2012; Zhang nitrogen and phosphorus) and contaminants (Nealson et al. 2015). In addition, BCC has been found to co-vary 1997; Bouskill et al. 2010). Sediment microorganisms, with metal concentrations in lake sediments (Cummings especially bacteria, play a dominant role in these critical et al. 2003; Bouskill et al. 2010; Sauvain et al. 2014). How- processes. Bacteria-mediated transformations in sedi- ever, the above studies and most available reports were ments lead to active exchange of energy and materials obtained based on investigations of multiple isolated lakes. with the water column and intimately connect sedimen- The relationship between BCC and environmental condi- tary processes with diverse aquatic ecosystem functions tions within individual freshwater lakes, especially those (Ranjard et al. 2000; Urakawa et al. 2000). with large volumes and surface areas has not been fully understood (Yannarell and Triplett 2004; Bouzat et al. 2013). Alternatively, whether environmental factors apply similar impacts on BCC in main lake area and estuarine *Correspondence: [email protected]; [email protected] 1 College of Life Science, Nanchang University, No. 999, Xuefu da Road, zone remain unclear. Hongutang New District, Nanchang 300031, Jiangxi, China Poyang Lake (28°52′21″–29°06′46″N, 116°10′24″– 3 Department of Biological Sciences, Kent State University, No. 800 E. 116°23′50″E), located in northern Jiangxi Province, is the Summit Street, Kent, OH 44240, USA Full list of author information is available at the end of the article largest freshwater lake in China with a storage capacity of © 2016 Kou et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Kou et al. SpringerPlus (2016) 5:401 Page 2 of 9 2.95 billion m3 (Fig. 1). The lake covers an area of 4125 km2 chosen to cover both of the main basins of the lake and the and has an average depth of 5.1 m. Poyang Lake is a mouths of major rivers that discharge into Poyang Lake, throughput type of lake, mainly collect freshwater from including two sites from main basin of the lake, i.e., Site tributary rivers, including the Gan, Fu, Xiu, Xin and Rao 1 in Songmenshan Region (29°12′26.9″N, 116°11′28.0″E), Rivers, and discharging into the Yangtze River. In recent and Site 4 in Nanjishan Region (28°55′00.1″N, years, natural and anthropogenic inputs of nutrients and 116°16′44.4″E); four sites from the lake estuaries (mouths xenobiotics have consistently increased. As a result, a of influx rivers), i.e., Site 2 (29°11′27.4″N, 116°00′33.3″E), decreasing gradient of nutrients and heavy metals along Site 3 (28°59′10.6″N, 116°40′10.6″E), Site 5 (28°39′54.4″N, transects from estuaries to main lake basins has estab- 116°9′31.9″E) and Site 6 (28°43′42.2″N, 116°24′34.8″E) lished (Liu et al. 2012; Zhang et al. 2014; Wang and Liang from Xiu, Rao, Fu and Xin River to Poyang Lake, 2015). This may result in spatial variations of sediment respectively. BCCs and their biogeochemical activities, which may in At each sampling site, triplicate surface sediment sam- turn impact the lake ecosystem function. However, so far ples were taken with a grab sampler to obtain a total of 18 no study has been done on sediment BCC in Poyang Lake. samples. Samples were transferred into sterile polyethyl- In this study, 16S rRNA gene-based quantitative PCR ene ziplock bags, put on ice and immediately transported and pyrosequencing were used to examine sediment to laboratory. Large organic debris was removed from the BCCs in Poyang Lake. Our specific goals were to (1) sediments with sterile forceps. Afterwards, samples were investigate horizontal dynamics of BCCs (i.e., relative divided into two aliquots. One aliquot was processed abundance and diversity), (2) examine the potential cor- immediately for measurements of sediment property var- relations between BCCs and environmental factors. iables; and the other aliquot was stored in sterile polypro- pylene tubes at 80 °C for molecular analysis. Methods − Study sites and sample collection Measurement of sediment properties Surface sediments (0–5 cm) were collected in May 2011 Sediment pH was measured on sediment slurry at a 1:2.5 from six sites in Poyang Lake (Fig. 1). These sites were (w/v) sediment: distilled water ratio using a FE20K pH meter (Mettler Toledo) (Rayment and Higginson 1992). For the measurement of organic matter, the dry matter content of sediment was determined after oven-dried at 105 °C for 24 h, then grinded using a mortar and pes- tle and sieved using a 0.25 mm mesh for the following measurements: sediment ash-free-dry-mass (AFDM) was obtained as the subsequent loss of weight after 4 h at 550 °C in a BF51800 muffle furnace (Thermal) (Hesse 1972). Total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) contents were analyzed by the Walkley–Black wet oxidation procedure, the microkjel- dahl method and the phosphomolybdic acid blue color method, respectively (Liu et al. 1996). The concentrations of heavy metals including copper (Cu), zinc (Zn), lead (Pb) and cadmium (Cd) were quantified using atomic absorption spectrophotometry after microwave digestion of samples. Briefly, 0.5 g of sieved and dried sediment was added into 9 ml concentrated nitric acid plus 3 ml concentrated hydrochloric acid at 175 °C for 10 min (US EPA 2007). After cooling down, the extracts were centri- fuged at 3000 rpm for 5 min; supernatant was analyzed using an AA800 atomic absorption spectrophotometer (PerkinElmer). DNA extraction and quantitative PCR Fig. 1 Sampling sites in Poyang Lake. 1 Songmenshan Region, 2 Xiu Microbial genomic DNA was extracted from 0.5 g sedi- River Estuary, 3 Rao River Estuary, 4 Nanjishan Region, 5 Fu River Estu- ment (wet-weight) using a Power Soil DNA extraction ary, 6 Xin River Estuary kit (MoBio) following the manufacturer’s instructions. Kou et al. SpringerPlus (2016) 5:401 Page 3 of 9 The obtained DNA was used as templates for quantita- annotated as chloroplasts and archaea were ignored in tive polymerase chain reaction (qPCR) to determine the further analyses. copy numbers of bacterial 16S rRNA genes. qPCR was Pyrotag sequences were deposited in the NCBI performed with the primer set Eub338F/Eub518R (Fierer Sequence Read Archive (SRA) under the project acces- et al. 2005). Standard curves ranging from 105 to 109 gene sion number SRP033375. copies per μl were obtained by a tenfold serial dilution of linearized plasmids (Takara) containing cloned 16SrRNA Statistical analysis genes that were amplified from Escherichia coli DNA. Physical and chemical variations among sediment sam- R2 value for the standard curves was 0.98, the slope was ples were analyzed using principal components analy- −3.15, which corresponded to an estimated amplifica- sis (PCA) by Canoco 5.0 (Biometrics). Differences of tion efficiency of 104 %. All DNA samples were processed sediment environmental variables and copy numbers of along with negative controls and standards. bacterial 16S rRNA genes among sampling sites were assessed using one-way ANOVA by SPSS 19.0 software Pyrosequencing of bacterial 16S rRNA genes package. The level of statistical significance was p < 0.05. The V4–V6 region of the 16S rRNA gene was PCR Based on taxonomic annotation, sequences were amplified from extracted DNA using universal primers grouped at the order level to construct rarefaction curves 530F and 1100R (Turner et al.
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